RJafroc (version 1.3.2)

PlotEmpiricalOperatingCharacteristics: Plot empirical operating characteristics, ROC, FROC or LROC

Description

Plot empirical operating characteristics (operating points connected by straight lines) for specified modalities and readers, or, if desired, plots (no operating points) averaged over specified modalities and / or readers.

Usage

PlotEmpiricalOperatingCharacteristics(
  dataset,
  trts = 1,
  rdrs = 1,
  opChType,
  legend.position = c(0.8, 0.2)
)

Arguments

dataset

Dataset object.

trts

List or vector: integer indices of modalities to be plotted. Default is 1.

rdrs

List or vector: integer indices of readers to be plotted. Default is 1.

opChType

Type of operating characteristic to be plotted: "ROC", "FROC", "AFROC", "wAFROC", "AFROC1", "wAFROC1", or "LROC".

legend.position

Where to position the legend. The default is c(0.8, 0.2), i.e., 0.8 rightward and 0.2 upward (the plot is a unit square).

Value

A ggplot2 object containing the operating characteristic plot(s) and a data frame containing the points defining the operating characteristics.

Plot

ggplot2 object. For continuous or averaged data, operating characteristics curves are plotted without showing operating points. For binned (individual) data, both operating points and connecting lines are shown. To avoid clutter, if there are more than 20 operating points, they are not shown.

Points

Data frame with four columns: abscissa, ordinate, class (which codes modality and reader) and type, which can be "individual", "continuous", i.e., more than 20 operating points, or "rdrAveraged".

Details

The trts and rdrs are vectors or lists of integer indices, not the corresponding string IDs. For example, if the string ID of the first reader is "0", the value in rdrs should be 1 not 0. The legend will display the string IDs.

If both of trts and rdrs are vectors, all combinations of modalities and readers are plotted. See Example 1.

If both trts and rdrs are lists, they must have the same length. Only the combination of modality and reader at the same position in their respective lists are plotted. If some elements of the modalities and / or readers lists are vectors, the average operating characteristic over the implied modalities and / or readers are plotted. See Example 2.

For LROC datasets, opChType can be "ROC" or "LROC".

Examples

# NOT RUN {
## Example 1
## Plot individual empirical ROC plots for all combinations of modalities
## 1 and 2 and readers 1, 2 and 3. Six operating characteristics are plotted.

ret <- PlotEmpiricalOperatingCharacteristics(dataset = 
dataset02, trts = c(1:2), rdrs = c(1:3), opChType = "ROC")
print(ret$Plot)

## Example 2
## Empirical ROC, FROC, AFROC and wAFROC plots. Each plot consists of
## three sub-plots (see Example 3 for correspondences between indices and  
## string identifiers for modalities and readers):
## (1) sub-plot, with operating points, for the 1st modality (string ID "1") and the 2nd 
## reader (string ID "3"), labeled M:1 R:3 
## (2) sub-plot, no operating points, for the 2nd modality (string ID "2") AVERAGED 
## over the 2nd and 3rd readers (string IDs "3" and "4"), labeled M:2  R: 3 4 
## (3) sub-plot, no operating points, AVERAGED over the first two modalities 
## (string IDs "1" and "2") AND over the 1st, 2nd and 3rd readers 
## (string IDs "1", "3" and "4"), labeled M: 1 2  R: 1  3 4 

plotT <- list(1, 2, c(1:2))
plotR <- list(2, c(2:3), c(1:3))
ret <- PlotEmpiricalOperatingCharacteristics(dataset = dataset04, 
   trts = plotT, rdrs = plotR, opChType = "ROC")
print(ret$Plot)

ret <- PlotEmpiricalOperatingCharacteristics(dataset = dataset04, trts = plotT, 
   rdrs = plotR, opChType = "FROC")               
print(ret$Plot)

ret <- PlotEmpiricalOperatingCharacteristics(dataset = dataset04, trts = plotT, 
   rdrs = plotR, opChType = "AFROC")
print(ret$Plot)

ret <- PlotEmpiricalOperatingCharacteristics(dataset = dataset04, trts = plotT, 
   rdrs = plotR, opChType = "wAFROC")                  
print(ret$Plot)

##Example 3
## Correspondences between indices and string identifiers for modalities and 
## readers in this dataset. Apparently reader "2" did not complete the study.

str(dataset04)

## List of 8
## NL          : num [1:5, 1:4, 1:200, 1:7] -Inf -Inf 1 -Inf -Inf ...
## LL          : num [1:5, 1:4, 1:100, 1:3] 4 5 4 5 4 3 5 4 4 3 ...
## $ lesionVector   : int [1:100] 1 1 1 1 1 1 1 1 1 1 ...
## $ lesionID    : num [1:100, 1:3] 1 1 1 1 1 1 1 1 1 1 ...
## $ lesionWeight: num [1:100, 1:3] 1 1 1 1 1 1 1 1 1 1 ...
## $ dataType    : chr "FROC"
## $ modalityID  : chr [1:5] "1" "2" "3" "4" "5"
## $ readerID    : chr [1:4] "1" "3" "4" "5"

# }